I suffer from this eye thing. I shoot right handed, and am left eye dominant. I suffer because I've always shot guns my entire life thru my RIGHT eye, before I knew I was left eye dominant.
I now try to make sure my left eye is over the cue...and you will find me routinely closing my right eye for a second during a stroke just to verify alignment, if my head is out of position, and my brain is grabbing my right eye...I can tell immediately when I close my right eye...that I'm gonna miss. I simply re-align, using only my D eye, open both eyes, and fire it in.
I've found no real way of avoiding my brain from gravitating to my right eye, I've only found ways to identify and correct quickly before it costs me a match. Some nights I don't have any problems, other nights, I just can't get away from it.